Question: Download reference mitochondria sequence
0
gravatar for cnr.lwlss
12 months ago by
cnr.lwlss0
United Kingdom
cnr.lwlss0 wrote:

Is there a way to download individual mitochondrial sequences from NCBI without having to scrape from their webpages or to download thousands of other sequences alongside. Is there some programmatic way to access these fasta data, for example:

https://www.ncbi.nlm.nih.gov/nuccore/NC_012920.1?report=fasta

sequence • 522 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by cnr.lwlss0
1
gravatar for cnr.lwlss
12 months ago by
cnr.lwlss0
United Kingdom
cnr.lwlss0 wrote:

Following this post:

curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_012920.1&rettype=fasta&retmode=text" >mtDNA.fa
ADD COMMENTlink modified 12 months ago • written 12 months ago by cnr.lwlss0
2
gravatar for genomax
12 months ago by
genomax62k
United States
genomax62k wrote:

You can use "Send to" drop down on that page to send the data to a file. No scraping needed.

If you have many of these to get then using NCBI eUtils is the best option. For example for the link you posted you can do this

efetch -db nuccore -id NC_012920.1 -format fasta > NC_012920.fa
ADD COMMENTlink written 12 months ago by genomax62k

Thanks, but installing eutils as below failed with errors: "Is libxml2 installed?" (yes, it is...)

pip3 install eutils

Glad you mentioned eutils though, as it led me to find this post, which showed me how to build the URL in the answer below.

ADD REPLYlink written 12 months ago by cnr.lwlss0
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